Ischemic stroke is caused by an embolus or local thrombosis and results in neural tissue damage (an infarct) in the territory of the occluded cerebral artery. Current understanding of the mechanisms underlying infarct damage is based primarily on experimental models. Several genes/pathways have been identified that regulate the size (volume) of the infarct when ischemia is induced in genetically manipulated mouse models. Unfortunately, evidence based solely on gene knockout or transgenic mice does not always provide insight into mechanisms involved in the natural disease state. Gene deletion or transgenic over-expression creates an artificial physiologic state that can be far removed from that found in naturally occurring disease. We propose to identify novel genes/pathways involved in infarction using QTL mapping. In the well-established focal cerebral ischemia mouse model of infarction, different inbred mouse strains exhibit robust differences in infarct volume. We have completed the largest known strain survey for this phenotype. The differences in infarct volume are highly reproducible within each strain, and between certain strains, very large (up to 700%). We have exploited these differences to map a natural genetic determinant of infarct volume. In an F1 intercross between B6 and BALB/c, we have mapped a locus on distal chromosome 7 that contributes over 50% of the observed variation in infarct volume. This single natural allele shows an effect on infarct volume that is larger than that observed for most published knockout or transgenic lines. We have validated the presence of this locus using chromosome substitution strains. Furthermore, by exploiting ancestral haplotype sharing patterns in 16 inbred strains, we have fine-mapped this locus to haplotype blocks covering only six genes. In this application, we propose to identify the gene underlying the chromosome 7 locus using molecular genetic and functional assays for the six genes. In parallel, we propose to determine the mechanism behind the chromosome 7 locus using anatomic and metabolic studies of CSS and congenic lines that will isolate the effects of this single locus. In the final aim we will map and identify new genes that also strongly influence infarct volume, employing crosses between phenotypically divergent inbred strains that do not differ at the chromosome 7 locus. The identification of novel, natural alleles modulating infarct volume will provide new and physiologically relevant insight into the pathways and mechanisms involved in infarction. In the long-term, this work may provide novel targets for therapeutic intervention of ischemic stroke. PUBLIC HEALTH RELEVANCE: Ischemic stroke results in brain tissue damage (an infarct) near the site of the blocked artery. We propose to identify genes that regulate this process by exploiting natural variation in infarct size in different mouse strains. The identification of new genes regulating infarct size will provide new insight into the pathways and mechanisms involved in infarction, and in the long-term, provide novel targets for therapeutic intervention of ischemic stroke.